About: Evolution of Genome Size and Complexity in the Rhabdoviridae

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Evolution of Genome Size and Complexity in the Rhabdoviridae
Creator	Walker, Peter Vasilakis, Nikos Firth, Cadhla Guzman, Hilda Gorbalenya, Alexander Tesh, Robert Holmes, Edward Wood, Thomas Blasdell, Kim Paradkar, Prasad Widen, Steven
source	PMC
abstract	RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.
has issue date	2015-02-13(xsd:dateTime)
bibo:doi	10.1371/journal.ppat.1004664
bibo:pmid	25679389
has license	cc-by
sha1sum (hex)	997f6355fdf8531d31a8bdadd1067f651e2e3d41
schema:url	https://doi.org/10.1371/journal.ppat.1004664
resource representing a document's title	Evolution of Genome Size and Complexity in the Rhabdoviridae
has PubMed Central identifier	PMC4334499
has PubMed identifier	25679389
schema:publication	PLoS Pathog
resource representing a document's body	covid:997f6355fdf8531d31a8bdadd1067f651e2e3d41#body_text
is schema:about of	named entity 'strategies' named entity 'complexity' named entity 'families' named entity 'genes' named entity 'discontinuous' named entity 'evolution' named entity 'Changes' named entity 'manner' named entity 'viruses' named entity 'involving' named entity 'evolution' named entity 'genome' named entity 'conduct' named entity 'EXPANSION' named entity 'TO IDENTIFY' named entity 'MAY BE' named entity 'RESULTING IN' named entity 'EXPRESSION' named entity 'FAMILIES' named entity 'GENOME SIZE' named entity 'SUPPORTED' named entity 'LENGTHS' named entity 'INVOLVING' named entity 'MUTATION RATE' named entity 'LIKELY' named entity 'ANALYSIS' named entity 'LARGE' named entity 'CONTRACTION' named entity 'CONCLUDE' named entity 'RNA VIRUSES' named entity 'GENOME SIZE' named entity 'MONOPHYLETIC' named entity 'OCCURRENCE' named entity 'THESE' named entity 'ENCODED' named entity 'DETERMINED' named entity 'FRAME' named entity 'GENOME COMPLEXITY' named entity 'ASSIGNED' named entity 'MODEL' named entity 'ANIMAL' named entity 'OVERLAPPING' named entity 'FREQUENCY' named entity 'SEVEN' named entity 'RHABDOVIRIDAE' named entity 'SMALLEST' named entity 'PLASTICITY' named entity 'CONDUCT' named entity 'TERMINATION' named entity 'LOSS OF' named entity 'JUNCTION' named entity 'INCREASED' named entity 'PROTEIN ' named entity 'DIVERSITY' named entity 'NON-' named entity 'DIRECTION' named entity 'EVOLUTION' named entity 'COMMON' named entity 'RIBOSOMAL' named entity 'CHANGES' named entity 'CONSECUTIVE' named entity 'RHABDOVIRIDAE' named entity 'SCALE' named entity 'CENTRAL' named entity 'TO INCREASE' named entity 'ESTABLISHED' named entity 'COMPLEXITY' named entity 'TRANSCRIPTION' named entity 'STRATEGIES' named entity 'CLADE' named entity 'GENE'

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